schrodinger.application.desmond.kinetics.enhanced_sampling module

This module generates the Monte Carlo scheme for RAMD as a Desmond plugin. Functions here assist in generating an pot file, which contains m-expr instructions for gDesmond.

M-expr are instructiosn provided to the gDesmond kernal, to be executed on the compute device. See Desmond’s Users Guide for enhanced sampling plugin for M{eta}-expression (m-expr) syntax, supported function calls, atomic operators and examples.

schrodinger.application.desmond.kinetics.enhanced_sampling.mindist_mexpr(st: structure.Structure, asl_receptor: str, asl_ligand: str, mindist_cutoff=8.0) → str

This function generates an m-expression encoding for calculation of minimal distance between two selections. :return : a string encoding calculation of MinDist in m-expr format.

schrodinger.application.desmond.kinetics.enhanced_sampling.ramd_mexpr(asl_ligand: str, lagtime: float, lagdist: float, decorrelation_time: float, seed: int, spring: float, spring_increase_rate: float = 0.0, debug: bool = False) → str
Parameters

decorrelation_time – waiting time before RAMD starts.

:return : a string encoding Random Accelerated MD M-expression format.

schrodinger.application.desmond.kinetics.enhanced_sampling.setup_ramd(st: structure.Structure, pot_fn: str, cvseq_interval: float, asl_receptor: str, ramd_opts: dict, killnow_cutoff: int, debug: bool = False)
Parameters

  • pot_fn – Write generated M-expression pot_fn file to be read by Desmond workflow

  • cvseq_interval – interval in ps to write one of the RAMD output files in cvseq format.

  • debug – if True additional information will be printed in cvseq for troubleshooting and debugging purposes.